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<div class="title">moltk/Biosequence.hpp</div>  </div>
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<a href="Biosequence_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    Commercial users should ask about our dual licensing model.</span>
<a name="l00020"></a>00020 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00021"></a>00021 <span class="comment">*/</span>
<a name="l00022"></a>00022 
<a name="l00023"></a>00023 <span class="comment">/*</span>
<a name="l00024"></a>00024 <span class="comment"> * Biosequence.h</span>
<a name="l00025"></a>00025 <span class="comment"> *</span>
<a name="l00026"></a>00026 <span class="comment"> *  Created on: Oct 5, 2011</span>
<a name="l00027"></a>00027 <span class="comment"> *      Author: brunsc</span>
<a name="l00028"></a>00028 <span class="comment"> */</span>
<a name="l00029"></a>00029 
<a name="l00030"></a>00030 <span class="preprocessor">#ifndef BIOSEQUENCE_H_</span>
<a name="l00031"></a>00031 <span class="preprocessor"></span><span class="preprocessor">#define BIOSEQUENCE_H_</span>
<a name="l00032"></a>00032 <span class="preprocessor"></span>
<a name="l00033"></a>00033 <span class="preprocessor">#include &lt;sstream&gt;</span>
<a name="l00034"></a>00034 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00035"></a>00035 <span class="preprocessor">#include &lt;string&gt;</span>
<a name="l00036"></a>00036 <span class="preprocessor">#include &lt;iterator&gt;</span>
<a name="l00037"></a>00037 
<a name="l00038"></a>00038 <span class="keyword">namespace </span>moltk
<a name="l00039"></a>00039 {
<a name="l00040"></a>00040 
<a name="l00044"></a><a class="code" href="classmoltk_1_1BaseBiosequence.html">00044</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures.">BaseBiosequence</a>
<a name="l00045"></a>00045 {
<a name="l00046"></a>00046 <span class="keyword">public</span>:
<a name="l00047"></a>00047 
<a name="l00051"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html">00051</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html" title="Parent class for macromolecule sequence residues (nucleotides or amino acids)">BaseResidue</a>
<a name="l00052"></a>00052     {
<a name="l00053"></a>00053     <span class="keyword">public</span>:
<a name="l00054"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#aed773ae21d9267adcfebf533b38a2880">00054</a>         <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#aed773ae21d9267adcfebf533b38a2880">BaseResidue</a>() {}
<a name="l00055"></a>00055         <span class="keyword">virtual</span> <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#aca9c851b8f3d46dfe93ff6a316a51c59">get_one_letter_code</a>() <span class="keyword">const</span> = 0;
<a name="l00056"></a>00056         <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#a21a653fddb38c2312eeca3f197e6bbc8">get_residue_number</a>() <span class="keyword">const</span> = 0;
<a name="l00057"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#a988df56becfb00e5068c6b63b6625cde">00057</a>         <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#a988df56becfb00e5068c6b63b6625cde">operator char</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#aca9c851b8f3d46dfe93ff6a316a51c59">get_one_letter_code</a>();}
<a name="l00058"></a>00058 
<a name="l00059"></a>00059     <span class="keyword">private</span>:
<a name="l00060"></a>00060         <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#aed773ae21d9267adcfebf533b38a2880">BaseResidue</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html" title="Parent class for macromolecule sequence residues (nucleotides or amino acids)">BaseResidue</a>&amp;);
<a name="l00061"></a>00061     };
<a name="l00062"></a>00062 
<a name="l00063"></a>00063 
<a name="l00064"></a>00064 <span class="keyword">public</span>:
<a name="l00065"></a><a class="code" href="classmoltk_1_1BaseBiosequence.html#ab40016d2526566c4dc17b29eaeb3dc74">00065</a>     <a class="code" href="classmoltk_1_1BaseBiosequence.html#ab40016d2526566c4dc17b29eaeb3dc74">BaseBiosequence</a>() {}
<a name="l00066"></a><a class="code" href="classmoltk_1_1BaseBiosequence.html#a50d0c5d8f88038a316eb2cf1a4a8cb54">00066</a>     <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html#a50d0c5d8f88038a316eb2cf1a4a8cb54">~BaseBiosequence</a>() {}
<a name="l00067"></a>00067     <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html#aab2f57949c05883dc8ca85577d634f4d">write_to_stream</a>(std::ostream&amp; os) <span class="keyword">const</span>;
<a name="l00068"></a>00068     <span class="keyword">virtual</span> <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html#a837f45a8604c435855b00aa90ace5841">get_number_of_residues</a>() <span class="keyword">const</span> = 0;
<a name="l00069"></a>00069     <span class="keyword">virtual</span> <span class="keyword">const</span> BaseResidue&amp; <a class="code" href="classmoltk_1_1BaseBiosequence.html#ae966c9bf162db00c2d5a4898170538af">get_residue</a>(<span class="keywordtype">size_t</span> index) <span class="keyword">const</span> = 0;
<a name="l00070"></a>00070 
<a name="l00071"></a>00071 <span class="keyword">private</span>:
<a name="l00072"></a>00072     <a class="code" href="classmoltk_1_1BaseBiosequence.html#ab40016d2526566c4dc17b29eaeb3dc74">BaseBiosequence</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures.">BaseBiosequence</a>&amp;);
<a name="l00073"></a>00073 };
<a name="l00074"></a>00074 
<a name="l00075"></a>00075 
<a name="l00079"></a><a class="code" href="classmoltk_1_1BiosequenceResidue.html">00079</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1BiosequenceResidue.html" title="One residue in a macromolecule sequence (a nucleotide or amino acid)">BiosequenceResidue</a> : <span class="keyword">public</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures.">BaseBiosequence</a>::BaseResidue
<a name="l00080"></a>00080 {
<a name="l00081"></a>00081 <span class="keyword">public</span>:
<a name="l00082"></a><a class="code" href="classmoltk_1_1BiosequenceResidue.html#a14a2113ef99cd06846798a68df873a5b">00082</a>     <a class="code" href="classmoltk_1_1BiosequenceResidue.html#a14a2113ef99cd06846798a68df873a5b">BiosequenceResidue</a>(<span class="keywordtype">char</span> one_letter_code_param, <span class="keywordtype">int</span> residue_number_param)
<a name="l00083"></a>00083         : <a class="code" href="classmoltk_1_1BiosequenceResidue.html#aaf62de3105859d585605982f72e127e3">one_letter_code</a>(one_letter_code_param)
<a name="l00084"></a>00084         , <a class="code" href="classmoltk_1_1BiosequenceResidue.html#aadadea46d0a17dc35ff54f543e42f460">residue_number</a>(residue_number_param)
<a name="l00085"></a>00085     {}
<a name="l00086"></a><a class="code" href="classmoltk_1_1BiosequenceResidue.html#a5b9a2759b675c4ebd31e288bce9e6220">00086</a>     <a class="code" href="classmoltk_1_1BiosequenceResidue.html#a14a2113ef99cd06846798a68df873a5b">BiosequenceResidue</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1BiosequenceResidue.html" title="One residue in a macromolecule sequence (a nucleotide or amino acid)">BiosequenceResidue</a>&amp; rhs)
<a name="l00087"></a>00087         : <a class="code" href="classmoltk_1_1BiosequenceResidue.html#aaf62de3105859d585605982f72e127e3">one_letter_code</a>(rhs.<a class="code" href="classmoltk_1_1BiosequenceResidue.html#aaf62de3105859d585605982f72e127e3">one_letter_code</a>)
<a name="l00088"></a>00088         , <a class="code" href="classmoltk_1_1BiosequenceResidue.html#aadadea46d0a17dc35ff54f543e42f460">residue_number</a>(rhs.<a class="code" href="classmoltk_1_1BiosequenceResidue.html#aadadea46d0a17dc35ff54f543e42f460">residue_number</a>)
<a name="l00089"></a>00089     {}
<a name="l00090"></a><a class="code" href="classmoltk_1_1BiosequenceResidue.html#a3bcbd7c24c5df4fa8d6b5e64c77ea136">00090</a>     <span class="keyword">virtual</span> <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1BiosequenceResidue.html#a3bcbd7c24c5df4fa8d6b5e64c77ea136">get_one_letter_code</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1BiosequenceResidue.html#aaf62de3105859d585605982f72e127e3">one_letter_code</a>;}
<a name="l00091"></a><a class="code" href="classmoltk_1_1BiosequenceResidue.html#ad7a50af311f8d4d088fb2367e456569f">00091</a>     <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1BiosequenceResidue.html#ad7a50af311f8d4d088fb2367e456569f">get_residue_number</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1BiosequenceResidue.html#aadadea46d0a17dc35ff54f543e42f460">residue_number</a>;}
<a name="l00092"></a>00092 
<a name="l00093"></a>00093 <span class="keyword">protected</span>:
<a name="l00094"></a><a class="code" href="classmoltk_1_1BiosequenceResidue.html#aaf62de3105859d585605982f72e127e3">00094</a>     <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1BiosequenceResidue.html#aaf62de3105859d585605982f72e127e3">one_letter_code</a>;
<a name="l00095"></a><a class="code" href="classmoltk_1_1BiosequenceResidue.html#aadadea46d0a17dc35ff54f543e42f460">00095</a>     <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1BiosequenceResidue.html#aadadea46d0a17dc35ff54f543e42f460">residue_number</a>;
<a name="l00096"></a>00096 };
<a name="l00097"></a>00097 
<a name="l00098"></a>00098 
<a name="l00102"></a><a class="code" href="classmoltk_1_1Biosequence.html">00102</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a> : <span class="keyword">public</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures.">BaseBiosequence</a>, <span class="keyword">public</span> std::vector&lt;BiosequenceResidue&gt;
<a name="l00103"></a>00103 {
<a name="l00104"></a>00104 <span class="keyword">public</span>:
<a name="l00105"></a><a class="code" href="classmoltk_1_1Biosequence.html#ad5da6959d153abf84e135e4f21e68a8d">00105</a>     <span class="keyword">typedef</span> <a class="code" href="classmoltk_1_1BiosequenceResidue.html" title="One residue in a macromolecule sequence (a nucleotide or amino acid)">BiosequenceResidue</a> <a class="code" href="classmoltk_1_1Biosequence.html#ad5da6959d153abf84e135e4f21e68a8d">Residue</a>;
<a name="l00106"></a>00106 
<a name="l00107"></a>00107 <span class="keyword">public</span>:
<a name="l00108"></a><a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">00108</a>     <a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">Biosequence</a>() {}
<a name="l00109"></a>00109     <a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">Biosequence</a>(<span class="keyword">const</span> std::string&amp; sequence, <span class="keyword">const</span> std::string&amp; <a class="code" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">description</a> = <span class="stringliteral">&quot;&quot;</span>);
<a name="l00110"></a>00110     <a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">Biosequence</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> * sequence, <span class="keyword">const</span> std::string&amp; <a class="code" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">description</a> = <span class="stringliteral">&quot;&quot;</span>);
<a name="l00111"></a>00111     <a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">Biosequence</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a>&amp; rhs);
<a name="l00112"></a><a class="code" href="classmoltk_1_1Biosequence.html#a2fe7b008000e37c494f64d720651b165">00112</a>     <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1Biosequence.html#a2fe7b008000e37c494f64d720651b165">~Biosequence</a>() {}
<a name="l00113"></a>00113     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Biosequence.html#a9ed5ae7e9926b9b1034fdad564a56dcd">load_stream</a>(std::istream&amp; is);
<a name="l00114"></a>00114     <a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a>&amp; <a class="code" href="classmoltk_1_1Biosequence.html#a44a245f0fe1ad46f81c2d1fb243b0bec">load_fasta</a>(<span class="keyword">const</span> std::string&amp; file_name);
<a name="l00115"></a>00115     <a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a>&amp; <a class="code" href="classmoltk_1_1Biosequence.html#a44a245f0fe1ad46f81c2d1fb243b0bec">load_fasta</a>(std::istream&amp; is);
<a name="l00116"></a><a class="code" href="classmoltk_1_1Biosequence.html#ac990688fe005304a3dd512a616017c71">00116</a>     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1Biosequence.html#ac990688fe005304a3dd512a616017c71">get_number_of_residues</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> size(); }
<a name="l00117"></a><a class="code" href="classmoltk_1_1Biosequence.html#a7347126c11c30536dfc3b0214f0dcc44">00117</a>     <span class="keyword">const</span> <a class="code" href="classmoltk_1_1BiosequenceResidue.html" title="One residue in a macromolecule sequence (a nucleotide or amino acid)">Residue</a>&amp; <a class="code" href="classmoltk_1_1Biosequence.html#a7347126c11c30536dfc3b0214f0dcc44">get_residue</a>(<span class="keywordtype">size_t</span> ix)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> (*<span class="keyword">this</span>)[ix]; }
<a name="l00118"></a><a class="code" href="classmoltk_1_1Biosequence.html#a8290cae93ff500228664fbb4666777a3">00118</a>     std::string <a class="code" href="classmoltk_1_1Biosequence.html#a8290cae93ff500228664fbb4666777a3">get_description</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">description</a>;}
<a name="l00119"></a>00119 
<a name="l00123"></a>00123     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Biosequence.html#a443c6178002614e5dc4215360cd5d206" title="Write sequence in fasta format to a C++ stream.">write_fasta</a>(std::ostream&amp; os) <span class="keyword">const</span>;
<a name="l00127"></a>00127     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Biosequence.html#a443c6178002614e5dc4215360cd5d206" title="Write sequence in fasta format to a C++ stream.">write_fasta</a>(<span class="keyword">const</span> std::string&amp; file_name) <span class="keyword">const</span>;
<a name="l00131"></a>00131     std::string <a class="code" href="classmoltk_1_1Biosequence.html#a27052034d07465e3f009d621e6545fae" title="Create a string representing the sequence in fasta format.">fasta</a>() <span class="keyword">const</span>;
<a name="l00132"></a>00132 
<a name="l00136"></a>00136     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Biosequence.html#a8f94aee2ef34bfdd3886d8545e0b1d7c" title="Write a sequence string to a C++ stream.">write_sequence_string</a>(std::ostream&amp; os) <span class="keyword">const</span>;
<a name="l00137"></a>00137 
<a name="l00141"></a>00141     std::string <a class="code" href="classmoltk_1_1Biosequence.html#a30c32f6a3ce92b1b33dbd911653136d7" title="repr is a helper for the python __repr__ method.">repr</a>() <span class="keyword">const</span>;
<a name="l00142"></a>00142 
<a name="l00143"></a><a class="code" href="classmoltk_1_1Biosequence.html#a71b3d56cc0f8f3c90957efd3592ddd0b">00143</a>     <span class="keyword">inline</span> <span class="keyword">friend</span> std::ostream&amp; <a class="code" href="classmoltk_1_1Biosequence.html#a71b3d56cc0f8f3c90957efd3592ddd0b">operator&lt;&lt;</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a>&amp; seq)
<a name="l00144"></a>00144     {
<a name="l00145"></a>00145         seq.<a class="code" href="classmoltk_1_1Biosequence.html#a8f94aee2ef34bfdd3886d8545e0b1d7c" title="Write a sequence string to a C++ stream.">write_sequence_string</a>(os);
<a name="l00146"></a>00146         <span class="keywordflow">return</span> os;
<a name="l00147"></a>00147     }
<a name="l00148"></a>00148 
<a name="l00149"></a><a class="code" href="classmoltk_1_1Biosequence.html#a8e8f8370f1a4769c9ce2e6ae0f44fa1e">00149</a>     <span class="keyword">inline</span> <span class="keyword">friend</span> std::istream&amp; <a class="code" href="classmoltk_1_1Biosequence.html#a8e8f8370f1a4769c9ce2e6ae0f44fa1e">operator&gt;&gt;</a>(std::istream&amp; is, <a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a>&amp; seq)
<a name="l00150"></a>00150     {
<a name="l00151"></a>00151         seq.<a class="code" href="classmoltk_1_1Biosequence.html#a9ed5ae7e9926b9b1034fdad564a56dcd">load_stream</a>(is);
<a name="l00152"></a>00152         <span class="keywordflow">return</span> is;
<a name="l00153"></a>00153     }
<a name="l00154"></a>00154 
<a name="l00155"></a>00155 <span class="keyword">protected</span>:
<a name="l00156"></a><a class="code" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">00156</a>     std::string <a class="code" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">description</a>;
<a name="l00157"></a>00157 };
<a name="l00158"></a>00158 
<a name="l00159"></a>00159 } <span class="comment">// namespace moltk</span>
<a name="l00160"></a>00160 
<a name="l00161"></a>00161 <span class="preprocessor">#endif </span><span class="comment">/* BIOSEQUENCE_H_ */</span>
</pre></div></div>
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